BMRB Entry 16859

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16859

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Title:
Solution structure of the double PHD (plant homeodomain) fingers of human transcriptional protein DPF3b bound to a histone N-terminal H3 peptide
Deposition date:
2010-04-13
Original release date:
2010-09-03
Authors:
Zeng, Lei; Zhang, Qiang; Li, SiDe; Plotnikov, Alexander; Walsh, Martin; ZHOU, MING-MING
Citation:

Citation: Zeng, Lei; Zhang, Qiang; Li, SiDe; Plotnikov, Alexander; Walsh, Martin; ZHOU, MING-MING. "Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b"  Nature 466, 258-262 (2010).
PubMed: 20613843

Assembly members:

Assembly members:
histone_N-terminal_H3, polymer, 20 residues, 2231.623 Da.
double_PHD_fingers, polymer, 114 residues, 12746.515 Da.
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pGEX4T-1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
histone_N-terminal_H3: ARTKQTARKSTGGXAPRKQL
double_PHD_fingers: GSYCDFCLGGSNMNKKSGRP EELVSCADCGRSGHPTCLQF TLNMTEAVKTYKWQCIECKS CILCGTSENDDQLLFCDDCD RGYHMYCLNPPVAEPPEGSW SCHLCWELLKEKAS

Data sets:
Data typeCount
13C chemical shifts364
15N chemical shifts117
1H chemical shifts820

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1histone_N-terminal_H31
2double_PHD_fingers2
3ZINC ION_13
4ZINC ION_23
5ZINC ION_33
6ZINC ION_43

Entities:

Entity 1, histone_N-terminal_H3 20 residues - 2231.623 Da.

1   ALAARGTHRLYSGLNTHRALAARGLYSSER
2   THRGLYGLYALYALAPROARGLYSGLNLEU

Entity 2, double_PHD_fingers 114 residues - 12746.515 Da.

1   GLYSERTYRCYSASPPHECYSLEUGLYGLY
2   SERASNMETASNLYSLYSSERGLYARGPRO
3   GLUGLULEUVALSERCYSALAASPCYSGLY
4   ARGSERGLYHISPROTHRCYSLEUGLNPHE
5   THRLEUASNMETTHRGLUALAVALLYSTHR
6   TYRLYSTRPGLNCYSILEGLUCYSLYSSER
7   CYSILELEUCYSGLYTHRSERGLUASNASP
8   ASPGLNLEULEUPHECYSASPASPCYSASP
9   ARGGLYTYRHISMETTYRCYSLEUASNPRO
10   PROVALALAGLUPROPROGLUGLYSERTRP
11   SERCYSHISLEUCYSTRPGLULEULEULYS
12   GLULYSALASER

Entity 3, ZINC ION_1 - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: potassium phosphate 100 mM; DTT 2 mM; D2O 100%

sample_2: potassium phosphate 100 mM; DTT 2 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D_13C-Edited_13C/15N-filtered NOESTsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(COCA)CBsample_1isotropicsample_conditions_1

Software:

ARIA v2.2, Linge, O'Donoghue and Nilges - refinement

NMRPipe v2.3, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5.04, Johnson, One Moon Scientific - data analysis

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz
  • Bruker DRX 500 MHz

Related Database Links:

BMRB 16858 16858 16861 16865
PDB
GB AET74057 AAX20019 EDL02734 EGV99590 EHH28015 EHH63746
DBJ BAC30204
REF NP_001254554 NP_001267471 XP_001140541 XP_001254780 XP_001375927
SP P58269 Q92784
TPG DAA25179
AlphaFold P58269 Q92784

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks